Here are some answers to your questions:
1. What is the difference between a Scrum Master vs a PMI Agile certification?
The ScrumMaster Certification is offered by the ScrumAlliance.org and focuses primarily on the Scrum method. You earn it by attending a 2 day class and then taking a test, last time I checked the test was an all pass test. You cannot take the test without attending the 2 day workshop.
The PMI Agile Certification tests your knowledge of several Agile and Lean methods such as Scrum, XP, Kanban, Agile Requirements Modeling in addition to others. It also requires at least 1 year of experience with using Agile and more years as a Project Manager in general.
2. If I have a Scrum Master Certification what is the purpose of the PMI Agile certification?
The PMI Certification focuses on more than just Scrum, it covers most of the popular Agile methods so that is one decision point for you, do you want to be certified in Scrum or in Agile methods?. The other decision point is that the PMI certification has stronger qualifications of experience so I would actually compare it more to the Scrum Professional Certification not the ScrumMaster one, so do you or your organization put more weight on a certification that required 2 days of training and a test or on the PMI Agile Certification and the Scrum Professional Certification that require experience?
One last decision point for you is where you see your future going. If you are interested in completing all the ScrumAlliance.org certifications such as the CSP and CSC then you don't need the PMI certification, if you see yourself aligning with PMI in the future then you could consider the new certification.
I hope these points help you make your own decision in terms of which direction to take!
3. If I have a Scrum Master Certification and a PMP Certification does that automatically makes me a PMI agile certified?
Good try :-) No, unfortuantley, you still do need to register for the PMI Agile Certification and take the exam. You need to have 21 credits of Agile training so if you've already been to the 2 day ScrumMaster class you have 14 so you may need only 7 more unless you've attending any additional courses.
You can find more information on how and when to register for the test on this site: http://www.pmi.org/agile
Thanks for posting your questions!